Variant report

Variant	rs12703
Chromosome Location	chr1:76257892-76257893
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	POLR2A	chr1:76257436-76260415	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:76257827-76264091	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:76257824-76258312	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:76256751-76258578	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
7	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
9	POLR2A	chr1:76256556-76258577	U87	brain:	n/a	n/a
10	POLR2A	chr1:76257807-76258271	K562	blood:	n/a	n/a
11	POLR2A	chr1:76257031-76260129	K562	blood:	n/a	n/a
12	POLR2A	chr1:76257848-76258090	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:76257887-76264164	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:76257762-76263752	Hela-S3	cervix:	n/a	n/a
15	IRF1	chr1:76257636-76258173	K562	blood:	n/a	n/a
16	POLR2A	chr1:76257808-76258150	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:76257814-76258587	HCT-116	colon:	n/a	n/a
19	POLR2A	chr1:76257791-76258276	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr1:76257617-76258242	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:76256596-76258577	U87	brain:	n/a	n/a
22	POLR2A	chr1:76257762-76258228	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:76257800-76258091	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:76257831-76258110	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:76257838-76258044	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
27	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:76257798-76260132	K562	blood:	n/a	n/a
29	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
30	POLR2A	chr1:76257881-76260036	A549	lung:	n/a	n/a
31	HEY1	chr1:76257857-76258239	K562	blood:	n/a	n/a
32	POLR2A	chr1:76256643-76264175	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:76257012-76263648	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr1:76257332-76260436	U87	brain:	n/a	n/a
35	POLR2A	chr1:76257793-76257991	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr1:76250012-76264059	K562	blood:	n/a	n/a
37	POLR2A	chr1:76257855-76258044	HCT-116	colon:	n/a	n/a
38	POLR2A	chr1:76257740-76258148	K562	blood:	n/a	n/a
39	POLR2A	chr1:76257835-76258126	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:76257772-76260053	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:76251020-76258361	U87	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76257416..76260329-chr1:76260481..76263578,4	MCF-7	breast:
2	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
3	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:

No data

Variant related genes	Relation type
MSH4	TF binding region
RABGGTB	TF binding region
ENSG00000117054	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs1021462	0.83[CHB][hapmap]
rs10732724	0.82[JPT][hapmap]
rs10873724	0.93[ASN][1000 genomes]
rs10873727	0.95[ASN][1000 genomes]
rs10873728	0.95[ASN][1000 genomes]
rs10873735	0.86[ASN][1000 genomes]
rs10873738	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10873739	0.95[ASN][1000 genomes]
rs1093006	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1093009	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161447	0.82[JPT][hapmap]
rs11161465	0.81[JPT][hapmap]
rs11161600	0.82[ASN][1000 genomes]
rs11161602	0.85[JPT][hapmap]
rs11161605	0.81[ASN][1000 genomes]
rs11161700	0.95[ASN][1000 genomes]
rs11161704	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161731	0.82[JPT][hapmap]
rs11161790	0.85[ASN][1000 genomes]
rs11161795	0.85[ASN][1000 genomes]
rs11161887	0.81[JPT][hapmap]
rs1144328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144338	0.95[ASN][1000 genomes]
rs1144339	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144341	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1144342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1146572	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1146577	0.81[EUR][1000 genomes]
rs1146592	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146593	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1146602	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1146613	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146616	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1146625	0.91[ASN][1000 genomes]
rs1146642	1.00[YRI][hapmap]
rs1146645	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146648	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1146649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1146651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1146652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1146656	0.95[ASN][1000 genomes]
rs11579355	0.94[ASN][1000 genomes]
rs12021750	0.82[JPT][hapmap]
rs12022011	0.89[CHB][hapmap]
rs12024086	0.85[ASN][1000 genomes]
rs12024645	0.86[JPT][hapmap]
rs12027620	0.82[CHB][hapmap]
rs12033058	0.87[JPT][hapmap]
rs12044025	0.91[JPT][hapmap]
rs12045299	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12076093	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12078151	0.95[ASN][1000 genomes]
rs12081710	0.95[ASN][1000 genomes]
rs12090712	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12385715	0.95[ASN][1000 genomes]
rs12401729	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403889	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405178	0.95[ASN][1000 genomes]
rs12407107	0.86[JPT][hapmap]
rs12409592	0.81[JPT][hapmap]
rs1250875	0.85[ASN][1000 genomes]
rs1250876	0.81[JPT][hapmap]
rs1250877	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1250878	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1250881	0.90[ASN][1000 genomes]
rs1250882	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251065	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251077	0.82[ASN][1000 genomes]
rs1251078	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1251079	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1251270	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251272	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1251273	0.99[ASN][1000 genomes]
rs1251274	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1251275	0.95[ASN][1000 genomes]
rs12728962	0.82[ASN][1000 genomes]
rs12732495	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12732722	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12756349	0.82[ASN][1000 genomes]
rs12757213	0.82[ASN][1000 genomes]
rs1303870	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1323734	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1498313	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1603734	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1621198	0.84[ASN][1000 genomes]
rs1631498	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1689271	0.85[JPT][hapmap]
rs1694428	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs17097681	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs17097695	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1767459	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1770513	0.88[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1796812	0.81[JPT][hapmap]
rs1812589	0.95[ASN][1000 genomes]
rs1908089	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1960528	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2012536	1.00[ASN][1000 genomes]
rs2047435	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2307077	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2788655	0.83[ASN][1000 genomes]
rs34045364	0.94[ASN][1000 genomes]
rs34177389	0.94[ASN][1000 genomes]
rs35290302	0.81[JPT][hapmap]
rs35591768	0.94[ASN][1000 genomes]
rs36054685	0.91[ASN][1000 genomes]
rs3737574	0.86[JPT][hapmap]
rs3765682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3819949	0.81[JPT][hapmap]
rs4347163	0.82[ASN][1000 genomes]
rs4949884	0.95[ASN][1000 genomes]
rs5019550	0.95[ASN][1000 genomes]
rs56350137	0.95[ASN][1000 genomes]
rs5745314	0.87[JPT][hapmap]
rs5745321	1.00[YRI][hapmap]
rs5745327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5745334	0.87[JPT][hapmap]
rs5745343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5745353	0.82[ASN][1000 genomes]
rs5745354	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs5745392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5745448	0.81[JPT][hapmap]
rs5745451	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs5745465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5745523	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs5745532	0.82[CHB][hapmap]
rs5745542	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs5745546	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs61676733	0.95[ASN][1000 genomes]
rs6687882	0.86[CHB][hapmap]
rs6695055	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs696677	0.82[ASN][1000 genomes]
rs696679	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs699677	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs699683	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699824	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs699825	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7514912	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7516477	0.81[JPT][hapmap]
rs7525919	0.91[JPT][hapmap]
rs7548391	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7548991	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs814851	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs814855	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs814873	0.81[ASN][1000 genomes]
rs814874	0.81[ASN][1000 genomes]
rs815309	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs931506	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap]
rs9660848	0.82[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76252200-76258400	Weak transcription	Spleen	Spleen
2	chr1:76252400-76258800	Transcr. at gene 5' and 3'	K562	blood
3	chr1:76254000-76260000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:76254200-76258400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:76254200-76258600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
6	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
8	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:76254800-76258200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:76254800-76258400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:76254800-76262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:76255200-76261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
15	chr1:76255400-76262600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:76255400-76263000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
18	chr1:76255600-76263000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:76255600-76264000	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr1:76255800-76259400	Weak transcription	Fetal Brain Male	brain
21	chr1:76255800-76261600	Weak transcription	Fetal Heart	heart
22	chr1:76255800-76264000	Strong transcription	Brain Anterior Caudate	brain
23	chr1:76255800-76264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:76255800-76264200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:76255800-76264400	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:76256000-76262400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:76256000-76262800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:76256000-76264200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:76256000-76264200	Strong transcription	Fetal Thymus	thymus
30	chr1:76256000-76264400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:76256000-76264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:76256000-76264600	Strong transcription	Fetal Stomach	stomach
33	chr1:76256200-76259000	Strong transcription	Thymus	Thymus
34	chr1:76256200-76259600	Strong transcription	Lung	lung
35	chr1:76256200-76262600	Strong transcription	Fetal Kidney	kidney
36	chr1:76256200-76263000	Strong transcription	Ovary	ovary
37	chr1:76256400-76258200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:76256400-76258200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:76256400-76259600	Strong transcription	HSMMtube	muscle
40	chr1:76256400-76262400	Strong transcription	Fetal Brain Female	brain
41	chr1:76256400-76262800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:76256400-76262800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:76256400-76264400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:76256600-76258000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:76256600-76261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:76256600-76262400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:76256600-76262600	Strong transcription	Primary B cells from cord blood	blood
48	chr1:76256600-76262600	Strong transcription	HMEC	breast
49	chr1:76256600-76263000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:76256600-76263000	Strong transcription	Colon Smooth Muscle	Colon

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